Natura 2000 SDF Manager Tool Installation Guide and User Manual

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Natura 2000
SDF Manager

Tool

Installation Guide and
User Manual


European Environment Agency


Abstract

This document includes a guide for the usage of

the Nature 2000
SDF Manager

Tool.


Ver

Date

Author

Description

0.1

21/11/2011

Alberto Telletxea

atelletxea@bilbomatica.es

First version

1.1

14/12/2011

Alberto Telletxea

atelletxea@bilbomatica.es

Version
revised after
the Work Shop
held in
Copenhaguen

1.2

27/02/2012

Alberto Telletxea

atelletxea@bilbomatica.es

Extended for
the upgrade of
the software
version 2.0

2.0

1
9
/03/2012

Alberto Telletxea

atelletxea@bilbomatica.es

Jérôme Bailly Maitre

refportnatura2000@mnhn.fr

Version
revised for the
final releas
e



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1

INTRODUCTION

................................
................................
................................
..........

3

2

INSTALLATION GUIDE

................................
................................
................................
.

3

2.1

Prerequisites

................................
................................
................................
..........

4

2.1.1

Java Version

................................
................................
................................
........

4

2.1.2

.NET Framework

................................
................................
................................
..

4

2.1.3

MYSQL database

................................
................................
................................
..

4

2.1.4

SET UP HOST, USER and PASSWORD FOR MYSQL database

................................
...

5

2.2

Run the Manager Tool

................................
................................
............................

7

3

SOFTWARE REQUIREMENT
S

................................
................................
........................

9

3.1

Access versions

................................
................................
................................
......

9

3.2

Specifications for the directory name of the tool

................................
.....................

9

4

USER MANUAL

................................
................................
................................
...........

9

4.1

Manage SDFs:

................................
................................
................................
.........

9

4.1.1

Filter:

................................
................................
................................
.................

10

4.1.2

Edit a site:

................................
................................
................................
..........

11

4.1.3

Delete or duplicate site:

................................
................................
......................

14

4.2

Import SDFs:

................................
................................
................................
.........

15

4.3

Export SDFs:

................................
................................
................................
..........

17

4.4

Perform checks QA/QC:

................................
................................
.........................

19




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SDF

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1

INTRODUCTION

The present manual describes the functionality of the Natura 2
000
Manager

Tool.
This tool is
meant to report Natura 2000
s
ite

descriptive data to the European Commission.

The tool will support the following main functionality:



Manage SDFs (Standard Data Form): Allow users to edit already imported sites and create
new

sites based on the new SDFschema published at
:
http://bd.eionet.europa.eu/activities/Natura_2000/reference_portal



Import SDFs: Allow users to import in the a
pplication SDFs
for future

editing
from the
following formats:

o


Old Access Database schema

o

New Database Schema

o

New XML schema



Export SDFs: Allow users to export one or many SDFs
edited inside the tool to

the
following formats:

o

Old Access Database schema

o

New Database Schem
a

o

New XML schema



Perform Checks: Allow users to perform a quality assurance on the

content of

the sites
imported in the tool

(e.g. Use of unknown species name).



2

INSTALLATION GUIDE

These are the steps to follow for the
installation

of the
new SDF Manager

Tool.
Basically, these
steps refer to the prerequisites to be installed previous the execution of the tool.
Once all these
prerequisites

have been accomplished

and
the tool is launched properly;

the
se

mentioned
prerequisites

will not need to be
installed

again.

These prerequisites are three software products:



JAVA SDK (it has to be downloaded from the ORACLE official web site)



.Net Framework 4.0 (it has to be downloaded from the Microsoft official web site)



MySQL (this software
can be downloaded from the N
atura 2000 Reference Portal
-

http://bd.eionet.europa.eu/activities/Natura_2000/N2000_software
,

folder How_to_MySQL.zip)



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All these steps are for users using computers which
do not have MySQL and Java installed. If you
do not have these tools installed, please follow the complete set of instructions below.

2.1

P
REREQUISITES

2.1.1

Java Version

As we are dealing with a Java application, in order to make it work, it is necessary to instal
l the
Java
SDK
.

The JDK includes tools useful for
execution of tools

written in the Java programming language and

running on the JavaTM platform as the case of the Natura 2000 Manager Tool.

The Java version to be installed is
the
jdk 1.6.0
or higher, it c
an be downloaded from the Oracle
Sun homepage:
http://www.oracle.com/technetwork/java/javase/downloads/jre
-
6u29
-
download
-
513650.html
. The user only has to
select the
W
indows version and follow the available
deployment instructions.

Windows x86 Offline

16.12 MB



jre
-
6u29
-
windows
-
i586.exe


Note:
Users already using this version of Java

SDK
, please skip this step.

2.1.2

.NET
Framework

The
relational database

in which the information will be stored is MySQL. Previous to the
dep
loyment of this Database, it is mandatory to install
Microsoft .NET Framework 4
, available at:
http://www.mic
rosoft.com/download/en/details.aspx?id=17851

2.1.3

MYSQL

database

MySQL is an open source relational database used for the SDF Manager Tool.

The installation
package

for MySQL

is made available
in the Natura 2000 Reference Portal

(folder
How_to_MySQL.zip
)
. In a
ddition, a MySQL user manual
(
How_to_MySQL.doc
)
details steps to
install/update/delete MySQL.



The steps to follow are:



Open the f
ile

How_to_
MySQL.
zip
, availables in the Reference Portal
http://bd.eionet.europa.eu/activities/Natura_2000/N2000_software



Double click
mysql
-
installer
-
5.5.
24.1
.
msi
;



Follow the given installation instructions

(a detailed explanations is given in
How_to_
MySQL
.doc
)
;



The
root

user will be asked for a

password in order to be able to start the Import Tool.



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Note:
Users already using this version of MySQL can skip the installation process.


2.1.4

SET UP HOST, USER and
PASSWORD FOR MYSQL
database

The SDF Import Tool allows to be run against a MySQL database in
stalled locally in the same
machine where the tool is executed or against a MySQL database installed remotely in another
database server.

2.1.4.1

Local database set up:

Once the MySQL d
atabase has been installed

locally
, the user must inform the
SDF Manager

Tool
application of the

user and

password
used

for the DataBase
. In order to do so:



Go to
SDF_Manager_Tool_19_03_2012(v2)
/database
directory

of the tool.



Edit
the
file

sdf_database.properties

.



This file has two
sections:

o

LOCAL MYSQL

o

REMOTE MYSQL



By removing
the symbol
#, u
ncomment the parameters for “LOCAL MYSQL” section and
keep commented
(keeping the symbol #)
the parameters for the “REMOTE MYSQL”
section, and edit the parameters as you have set for the local installation:


o

host: localhost

o

port: 3306 (this
is the default port used by MySQL)

o

user=
XXXX

o

password=
XXX


See the capture below.




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ATURA
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2.1.4.2

Remote database set up:

In case you have in your organization a dedicated database server with MySQL, you can use it also
for the SDF Manager Tool.

In order to do so:



Go t
o
SDF_Manager_Tool_19_03_2012(v2)
/database
directory

of the tool.



Edit
the
file

sdf_database.properties

.



This file has two
sections:

o

LOCAL MYSQL

o

REMOTE MYSQL



Uncomment the parameters for “REMOTE MYSQL” section and keep commented the
parameters for the “L
OCAL MYSQL” section, and edit the parameters as your database
administrator have set for the remote installation:


o

host: XXXX

o

port: 3306 (this is the default port used by MySQL)

o

user=
XXXX

o

password=
XXX


See the capture below.



E.g. for
W
indows: the host a
dress (IP adress) can be found as following:

o

on the server, go to Start, then click on Run

o

write: cmd

o

write: ipconfig /all


See the captures below, the last one showing the host adress (IP adress)



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2.2

R
UN THE
M
ANAGER

T
OOL

If you have already installed the

tool you will need to DROP the SCHEMA from MySQL for the
Natura2000 DB. A screen shot with this operation is shown below.


Please NOTE, that this will delete all data from the mySQL database.

It is recomm
e
nded to export
the data before droping the SCHEMA
from MySQL (see the section 4.2 page 17)


There are two ways to drop down the schema

o

remote version:
from a SQL query

by writting

: drop database `natura2000`, then
execute the query

o

local version:
from MySQL Workbench
,

see the capture below





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Enter y
our password




Once having followed the previous steps, simply double clicking
SDF_Manager.jar

will

start the
Import Tool
.

Double click

C
lick

right on Natura 2000
then select ‘Drop schema’



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3

SOFTWARE REQUIREMENT
S

3.1

A
CCESS

VERSIONS

The software only supports
the following Microsoft Access v
ersions:



2003



2007



2010

3.2

S
PECIFIC
ATIONS FOR THE DIREC
TORY NAME OF THE TOO
L

There cannot be any spaces in the name of the directory of the tool.



4

USER MANUAL

4.1

M
ANAGE
SDF
S
:

The user will use this area of the application to create new SDFs or modify already imported SDFs.




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4.1.1

Filter:

This ca
pability allows users to search by different filter types inside the different sites that have
been already imported in the application. These are the filters that can be used in the application:

1.

General:



By SiteType



By SiteCode



By SiteName


2.

Geography:



By
Region



By Bioregion



By Area by Hectares



By Marine Area by Hectares


3.

Dates:



By Date Site Classified as SPA



By Date Site Proposed as SCI



By Date Site Confirmed as SCI



By Date Site Designated as SAC


4.

Species:



By Species Name



By Species Group



By Other Species
Name



By Other Species Group



By Sensitive Species (YES or NO)


5.

Habitats:



By Habitats Name



By Habitats Class





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Thi
s capture shows the window to apply filters for the searching of sites.


Keep in mind that you have to “Reset Filter” to go back to the origin
al situation where all of the
sites imported were shown in the list.

4.1.2

Edit a site:

The editor will allow user to create a new site and fullfil all the data associated for that site
through the different forms and also modify an existing one.

The different f
orms for the completion of the data are aligned with the new Natura 2000 SDF XML
schema. All this ancillary information is documented at the Natura 2000 Reference Portal:

http
://bd.eionet.europa.eu/activities/Natura_2000/reference_portal

The capture below shows the b
u
ttons to create a new SDF or for editing an existing one.



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When user click on “New”
,

a window will appear to assign a Sitecode (9 characters code).


Afterword
s, the user will go through the different sections that the SDF
proposes
:



Site identification



Location



Ecological info



Description



Protection status



Man
a
gement



Maps



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The user will be able to do certain operations during the edition process:

1.

View the site

in the SDF Print form (by clicking in “View”)

or generate a PDF
. The print form
will be shown in a web browser:


The tool supports the following browsers:



Chrome (any version)



Internet Explorer 7 or higher



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FireFox 3.6 or higher

2.

Validate the site being ed
ited against
the

schema (by clicking in “Edit”). The users wil
l

be
inform
ed

through a log of the different errors of the data edited against the schema.

3.

Save (by clicking in “Save”). This will save the data edited in the local database. The user
can go bac
k to the site later if the action save has been ex
e
cute
d
.

4.

Export (by clicking in “Export”). The user can export a single site to the new SDF XML
format in the hard drive of the computer used.


4.1.3

Delete or duplicate site:

The user will be allowed to:



delete a

single site or multiple sites



duplicate a site

This functionality allows the user to manage better the list of sites that she/he wants finally to
export.








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4.2

I
MPORT
SDF
S
:


The user will
be
able to import in the tool existing SDFs in other formats.
The import process will
store the data in the local database of the application
,

allowing the user to edit the imported data
inside the tool.

The import formats that the tool allows are:



XML (following New SDF schema)



MS Access DB (old template)



MS Access
DB (new template)

The user will be allowed to browse in her/his local directories and select the file to import.
Besides, the user will set up the encoding system for the import.

Note
: We recommend the use of “ISO
-
8859
-
1” for MS Access DB and “UTF
-
8” for X
MLs.

For MS
with linguistic characters (e.g. SK, HU, etc), they should try with “ISO
-
8859
-
2” and
“UTF
-
8”
.


During the import process, system informs at every moment about the site processing.

An information message is displayed when import process finishes

successfully.




See the capture below with these settings.



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4.3

E
XPORT
SDF
S
:



The user will
be
able to export
from

the tool the imported/edited SDFs. The export process will
create a file and store it in the local hard drive of the computer.

Th
e export formats that the tool allows are:



XML (following New SDF schema)



MS Ac
ces
s DB (new template)


See the capture with interface of the export functionality.



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The tool will validate first the different SDFs to be exported against the XML schema. All
the errors
encountered will be notified to the user through a log

file
.













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4.4

P
ERFORM CHECKS
QA/QC:


The user will be able to check the consistency of the
conten of the
data by checking the data
edited in the tool based on several statements (e.g. u
nknown species name used). The user can fix
the issues encountered later
with

the tool

editor
.

See
the
capture below: